Contacts of the helix formed by residues 4770 - 4784 (chain B) in PDB entry 6X34
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP4770 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4706B THR* 5.4 4.9 - - + -
4707B PRO* 5.6 6.1 - - + -
4768B SER 3.7 3.3 + - - +
4769B ILE* 1.3 75.6 - - - +
4771B VAL* 1.3 61.0 + - - +
4772B LYS* 4.3 3.8 - - + +
4773B TYR* 3.9 26.1 - - + +
4774B GLN* 2.9 31.8 + - - +
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Residues in contact with VAL4771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4769B ILE 4.3 0.4 - - - -
4770B ASP* 1.3 72.2 - - - +
4772B LYS* 1.3 75.0 + - + +
4774B GLN* 4.2 4.9 - - - +
4775B ILE* 3.4 23.8 + - + +
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Residues in contact with LYS4772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4702B LEU* 3.6 15.9 - - - +
4705B ASN* 3.5 58.3 + - - +
4706B THR* 4.2 12.2 + - + +
4707B PRO* 4.9 8.1 - - + +
4770B ASP* 3.2 3.2 - - + +
4771B VAL* 1.3 89.5 - - + +
4773B TYR* 1.3 59.8 + - - +
4775B ILE* 3.9 3.8 + - - +
4776B TRP* 3.7 15.6 + - - +
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Residues in contact with TYR4773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4668B ILE* 5.5 3.7 - - + +
4703B VAL* 5.7 1.8 - - + -
4706B THR* 4.2 22.2 + - + -
4708B SER 5.5 1.1 - - - -
4710B PRO* 3.6 38.1 - - + +
4712B ASN* 4.8 5.9 + - - -
4770B ASP* 3.4 23.6 + - + +
4772B LYS* 1.3 79.4 - - - +
4774B GLN* 1.3 64.3 + - + +
4775B ILE 3.2 0.4 - - - -
4776B TRP* 4.2 10.9 - + - +
4777B LYS* 2.9 51.5 + - + +
4778B PHE* 6.4 2.0 - + - -
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Residues in contact with GLN4774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4769B ILE* 6.3 1.8 - - + -
4770B ASP 2.9 18.8 + - - +
4771B VAL* 4.2 5.8 - - - +
4773B TYR* 1.3 82.5 - - + +
4775B ILE* 1.3 60.8 + - - +
4777B LYS* 4.8 1.6 - - - -
4778B PHE* 3.3 49.8 + - + +
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Residues in contact with ILE4775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4699B TRP* 3.5 19.6 - - + -
4702B LEU* 5.2 7.9 - - + -
4771B VAL* 3.4 16.9 + - + +
4772B LYS* 4.3 4.0 - - - +
4773B TYR 3.2 0.4 - - - -
4774B GLN* 1.3 78.8 - - - +
4776B TRP* 1.3 58.3 + - - +
4778B PHE* 5.4 0.2 - - - -
4779B GLY* 3.1 19.8 + - - -
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Residues in contact with TRP4776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4668B ILE* 4.7 18.4 - - + -
4671B ARG* 3.9 31.7 - - + +
4672B GLU* 5.1 15.0 - - + -
4675B LEU* 4.9 8.1 - - + -
4699B TRP* 3.3 37.5 + + - +
4700B ASP* 3.6 13.8 - - + +
4702B LEU* 3.9 14.3 - - + +
4703B VAL* 3.5 49.8 - - + +
4710B PRO* 4.3 22.0 - - + -
4772B LYS 3.7 10.5 + - - +
4773B TYR* 3.5 10.2 + + - +
4774B GLN 3.5 0.2 - - - -
4775B ILE* 1.3 77.2 - - - +
4777B LYS* 1.3 78.8 + - + +
4780B VAL* 3.3 27.2 + - + +
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Residues in contact with LYS4777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4668B ILE* 4.4 9.2 - - + +
4773B TYR* 2.9 48.5 + - + +
4774B GLN* 4.6 0.9 - - - +
4776B TRP* 1.3 90.6 - - + +
4778B PHE* 1.3 72.9 + - + +
4779B GLY 3.3 0.7 + - - -
4780B VAL* 3.4 6.1 + - - +
4781B ILE* 3.2 22.2 + - - +
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Residues in contact with PHE4778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4660B ASN* 6.3 1.3 - - - -
4773B TYR* 6.4 2.0 - + - -
4774B GLN* 3.3 37.3 + - + +
4775B ILE 4.9 0.2 - - - +
4777B LYS* 1.3 83.5 - - + +
4779B GLY* 1.3 60.8 + - - +
4781B ILE* 3.5 10.7 + - + +
4782B PHE* 3.2 52.1 + + + -
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Residues in contact with GLY4779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4699B TRP* 3.6 22.4 - - - -
4775B ILE 3.1 21.8 + - - -
4777B LYS 3.2 0.6 - - - -
4778B PHE* 1.3 78.5 - - - +
4780B VAL* 1.3 59.0 + - - +
4782B PHE* 3.6 4.4 + - - +
4783B THR* 2.8 33.6 + - - +
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Residues in contact with VAL4780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4667B VAL* 5.6 7.0 - - + +
4668B ILE* 4.9 7.9 - - + -
4671B ARG* 3.4 48.9 - - + +
4699B TRP* 4.3 15.5 - - + -
4776B TRP* 3.3 23.8 - - + +
4777B LYS* 3.4 6.8 + - - +
4778B PHE 3.4 0.2 - - - -
4779B GLY* 1.3 75.6 - - - +
4781B ILE* 1.3 68.0 + - + +
4783B THR* 3.2 8.5 + - - +
4784B ASP* 2.9 30.1 + - + +
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Residues in contact with ILE4781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4660B ASN* 6.2 1.1 - - - +
4664B VAL* 3.6 35.2 - - + -
4667B VAL* 4.2 13.7 - - + -
4668B ILE* 3.8 24.5 - - + -
4777B LYS 3.2 16.4 - - - +
4778B PHE* 3.5 13.0 + - + +
4779B GLY 3.3 0.6 - - - -
4780B VAL* 1.3 81.5 - - + +
4782B PHE* 1.3 65.7 + - + +
4784B ASP* 3.4 10.2 + - + +
4787B PHE* 3.2 61.6 - - + +
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Residues in contact with PHE4782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4778B PHE* 3.2 40.3 + + + +
4779B GLY* 4.2 5.4 - - - +
4781B ILE* 1.3 80.2 - - + +
4783B THR* 1.3 60.9 + - + +
4784B ASP 4.5 2.6 - - - +
4787B PHE* 4.0 27.2 - + - -
4788B LEU* 4.8 8.8 - - - +
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Residues in contact with THR4783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4699B TRP* 6.2 4.9 - - + -
4779B GLY 2.8 22.3 + - - +
4780B VAL* 3.2 12.0 + - - +
4782B PHE* 1.3 80.0 - - + +
4784B ASP* 1.3 63.2 + - - +
4785B ASN* 3.6 2.1 + - - -
4788B LEU* 5.6 0.4 - - - -
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Residues in contact with ASP4784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4667B VAL* 5.8 8.5 - - + -
4780B VAL* 2.9 19.8 + - + +
4781B ILE* 3.4 15.7 + - + +
4783B THR* 1.3 78.0 - - - +
4785B ASN* 1.3 62.2 + - - +
4786B SER* 4.2 14.1 - - - +
4787B PHE* 4.2 6.1 - - + +
4788B LEU* 3.0 30.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il